chr8-129358168-C-T

Variant names:

• chr8-129358168-C-T
• rs7846684
• ENST00000446592.7:n.432-5188G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000446592.7(CCDC26):​n.432-5188G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,992 control chromosomes in the GnomAD database, including 26,569 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.59 (26569 hom., cov: 31)
• Consequence: CCDC26 ENST00000446592.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.680
• Publications: 3 publications found

Genes affected

CCDC26 (HGNC:28416): (CCDC26 long non-coding RNA)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.632 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CCDC26	NR_130917.1	n.432-5188G>A		intron_variant	Intron 3 of 3
CCDC26	NR_130918.1	n.209-5188G>A		intron_variant	Intron 2 of 2
CCDC26	NR_130919.1	n.363-5188G>A		intron_variant	Intron 3 of 3
CCDC26	NR_130920.1	n.380-5188G>A		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CCDC26	ENST00000446592.7	n.432-5188G>A		intron_variant	Intron 3 of 3	1
CCDC26	ENST00000523151.6	n.207-5188G>A		intron_variant	Intron 2 of 2	1
CCDC26	ENST00000520048.1	n.353-5188G>A		intron_variant	Intron 3 of 3	3

Frequencies

GnomAD3 genomes AF: 0.588 AC: 89311 AN: 151874 Hom.: 26557 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.588

Gnomad EAS AF: 0.471

Gnomad SAS AF: 0.555

Gnomad FIN AF: 0.680

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.582

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.588 AC: 89358 AN: 151992 Hom.: 26569 Cov.: 31 AF XY: 0.590 AC XY: 43852 AN XY: 74282

African (AFR) AF: 0.638 AC: 26451 AN: 41446

American (AMR) AF: 0.471 AC: 7187 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.588 AC: 2037 AN: 3466

East Asian (EAS) AF: 0.471 AC: 2431 AN: 5158

South Asian (SAS) AF: 0.556 AC: 2675 AN: 4812

European-Finnish (FIN) AF: 0.680 AC: 7186 AN: 10564

Middle Eastern (MID) AF: 0.599 AC: 176 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39491 AN: 67970

Other (OTH) AF: 0.580 AC: 1224 AN: 2110

Alfa AF: 0.576 Hom.: 43517

Bravo AF: 0.572

Asia WGS AF: 0.520 AC: 1808 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.92
DANN	Benign	0.32
PhyloP100		-0.68

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7846684; hg19: chr8-130370414;